In [1]:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
import re
from imp import reload
import h5py
In [2]:
import deltascope as cranium
import deltascope.alignment as ut
In [3]:
at = ".\\data\\28hpf\\AT\\Prob"
gfap = ".\\data\\28hpf\\Gfap\\Prob-yot-zrf-ilastik"
In [4]:
outdir = ".\\data\\28hpf\\Output-02-14-2019-yot-ilastik"
In [5]:
os.mkdir(outdir)
In [6]:
Dat = {}
for f in os.listdir(at):
if 'h5' in f:
num = re.findall(r'\d+',f.split('.')[0])[-1]
Dat[num] = os.path.join(at,f)
In [7]:
Dzrf = {}
for f in os.listdir(gfap):
if 'h5' in f:
num = re.findall(r'\d+',f.split('.')[0])[-1]
Dzrf[num] = os.path.join(gfap,f)
In [8]:
Dbat = {}
Dbzrf = {}
Data Preprocessing¶
In [9]:
klist = Dat.keys()
In [10]:
param = {
'gthresh':0.5,
'scale':[1,1,1],
'microns':[0.16,0.16,0.21],
'mthresh':0.5,
'radius':10,
'comp_order':[0,2,1],
'fit_dim':['x','z'],
'deg':2
}
In [11]:
%%time
for k in klist:
if k not in list(Dbat.keys()):
Dbat[k] = ut.preprocess(Dat[k],param)
Dbzrf[k] = ut.preprocess(Dzrf[k],param,pca=Dbat[k].pcamed,mm=Dbat[k].mm,vertex=Dbat[k].vertex)
print(k)
else:
print(k,'already processed')
In [12]:
def start(k):
return(ut.start(k,Dbat,[Dbzrf],im=True))
def save_both(k,dfa,dfb):
ut.save_both(k,dfa,dfb,outdir,'28hpf')
In [13]:
model = pd.DataFrame({'a':[],'b':[],'c':[]})
def save_model(k,mm,model):
row = pd.Series({'a':mm[0],'b':mm[1],'c':mm[2]},name=k)
model = model.append(row)
return(model)
In [14]:
def fit_model(axi,df,mm=None):
if mm == None:
mm = np.polyfit(df.x,df.z,2)
p = np.poly1d(mm)
xrange = np.arange(np.min(df.x),np.max(df.x))
axi.plot(xrange,p(xrange),c='m')
return(mm)
In [15]:
def pick_pts(x1,z1,vx,vz,x2,z2):
pts = pd.DataFrame({'x':[x1,vx,x2],'z':[z1,vz,z2]})
return(pts)
104¶
In [16]:
k,df,Ldf,ax = start('104')
In [17]:
mm = fit_model(ax[0,1],df)
In [18]:
model = save_model(k,mm,model)
115¶
In [19]:
k,df,Ldf,ax = start('115')
In [20]:
df1,Ldf1 = ut.zyswitch(df,Ldf)
ax = ut.make_graph([df1]+Ldf1)
In [21]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [22]:
save_both(k,df2,Ldf2[0])
In [23]:
model = save_model(k,mm,model)
10¶
In [24]:
k,df,Ldf,ax = start('10')
In [25]:
df1,Ldf1,pts,ax = ut.check_pts(df,Ldf,'z')
In [26]:
pts.iloc[1].x = -46
pts.iloc[1].z = 30
pts.iloc[0].z = 38
ax[0,1].scatter(pts.x,pts.z,c='y')
pts
Out[26]:
In [27]:
df2,Ldf2,ax = ut.revise_pts(df,Ldf,'z',pts=pts)
In [28]:
df3,Ldf3,mm,ax = ut.ch_vertex(df2,Ldf2)
In [29]:
save_both(k,df3,Ldf3[0])
In [30]:
model = save_model(k,mm,model)
116¶
In [31]:
k,df,Ldf,ax = start('116')
In [32]:
df1,Ldf1,ax,p = ut.check_yz(df,Ldf)
In [33]:
mm = [-1,0]
xrange = np.arange(-10,10)
ax[0,2].plot(xrange,np.poly1d(mm)(xrange),c='g')
Out[33]:
In [34]:
df2,Ldf2,ax,p = ut.check_yz(df,Ldf,mm=mm)
In [35]:
df3,Ldf3,mm,ax = ut.ch_vertex(df2,Ldf2)
In [36]:
save_both(k,df3,Ldf3[0])
In [37]:
model = save_model(k,mm,model)
16¶
In [38]:
k,df,Ldf,ax = start('16')
In [39]:
df1,Ldf1,pts,ax = ut.check_pts(df,Ldf,'z')
In [40]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [41]:
save_both(k,df2,Ldf2[0])
In [42]:
model = save_model(k,mm,model)
6¶
In [43]:
k,df,Ldf,ax = start('6')
In [44]:
mm = fit_model(ax[0,1],df)
In [45]:
save_both(k,df,Ldf[0])
In [46]:
model = save_model(k,mm,model)
119¶
In [47]:
k,df,Ldf,ax = start('119')
In [48]:
df1,Ldf1,ax,p = ut.check_yz(df,Ldf)
In [49]:
mm = [1.2,0]
xrange = np.arange(-5,5)
ax[0,2].plot(xrange,np.poly1d(mm)(xrange),c='y')
Out[49]:
In [50]:
df2,Ldf2,ax,p = ut.check_yz(df,Ldf,mm=mm)
In [51]:
df3,Ldf3,mm,ax = ut.ch_vertex(df2,Ldf2)
In [52]:
save_both(k,df3,Ldf3[0])
In [53]:
model = save_model(k,mm,model)
120¶
In [54]:
k,df,Ldf,ax = start('120')
In [55]:
mm = [-1/2,0]
xrange = np.arange(-5,5)
ax[0,2].plot(xrange,np.poly1d(mm)(xrange),c='y')
Out[55]:
In [56]:
df1,Ldf1,ax,p = ut.check_yz(df,Ldf,mm=mm)
In [57]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [58]:
pts = pick_pts(-35,15,0,-2,40,16)
ax[0,1].scatter(pts.x,pts.z,c='m',s=50)
Out[58]:
In [59]:
df3,Ldf3,mm,ax = ut.ch_vertex(df1,Ldf1,pts=pts)
In [60]:
save_both(k,df3,Ldf3[0])
In [61]:
model = save_model(k,mm,model)
14¶
In [62]:
k,df,Ldf,ax = start('14')
In [63]:
df1,Ldf1,pts,ax = ut.check_pts(df,Ldf,'z')
In [64]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [65]:
pts = pick_pts(-20,15,0,0,22,15)
ax[0,1].scatter(pts.x,pts.z,c='m',s=50)
Out[65]:
In [66]:
df3,Ldf3,mm,ax = ut.ch_vertex(df2,Ldf2,pts=pts)
In [67]:
save_both(k,df3,Ldf3[0])
In [68]:
model = save_model(k,mm,model)
8¶
In [69]:
k,df,Ldf,ax = start('8')
In [70]:
mm = [-2/5,0]
xrange = np.arange(-5,15)
ax[0,2].plot(xrange,np.poly1d(mm)(xrange),c='y')
Out[70]:
In [71]:
df1,Ldf1,ax,p = ut.check_yz(df,Ldf,mm=mm)
In [72]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [73]:
pts = pick_pts(-48,20,0,-2,48,20)
ax[0,1].scatter(pts.x,pts.z,c='m',s=50)
Out[73]:
In [74]:
df3,Ldf3,mm,ax = ut.ch_vertex(df2,Ldf2,pts=pts)
In [75]:
save_both(k,df3,Ldf3[0])
In [76]:
model = save_model(k,mm,model)
121¶
In [77]:
k,df,Ldf,ax = start('121')
In [78]:
df1,Ldf1 = ut.zyswitch(df,Ldf)
ax = ut.make_graph([df1]+Ldf1)
In [79]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [80]:
save_both(k,df2,Ldf2[0])
In [81]:
model = save_model(k,mm,model)
12¶
In [82]:
k,df,Ldf,ax = start('12')
In [83]:
save_both(k,df,Ldf[0])
In [84]:
mm = fit_model(ax[0,1],df)
In [85]:
model = save_model(k,mm,model)
117¶
In [86]:
k,df,Ldf,ax = start('117')
In [87]:
df1,Ldf1 = ut.zyswitch(df,Ldf)
ax = ut.make_graph([df1]+Ldf1)
In [88]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [89]:
save_both(k,df2,Ldf2[0])
In [90]:
model = save_model(k,mm,model)
5¶
In [91]:
k,df,Ldf,ax = start('5')
In [92]:
df1,Ldf1 = ut.zyswitch(df,Ldf)
ax = ut.make_graph([df1]+Ldf1)
In [93]:
pts = pick_pts(-35,10,-2,-6,30,10)
ax[0,1].scatter(pts.x,pts.z,c='m',s=50)
Out[93]:
In [94]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1,pts=pts)
In [95]:
save_both(k,df2,Ldf2[0])
In [96]:
model = save_model(k,mm,model)
4¶
In [97]:
k,df,Ldf,ax = start('4')
In [98]:
mm = fit_model(ax[0,1],df)
In [99]:
save_both(k,df,Ldf[0])
In [100]:
model = save_model(k,mm,model)
112¶
In [101]:
k,df,Ldf,ax = start('112')
In [102]:
mm = fit_model(ax[0,1],df)
In [103]:
save_both(k,df,Ldf[0])
In [104]:
model = save_model(k,mm,model)
118¶
In [105]:
k,df,Ldf,ax = start('118')
In [106]:
mm = [-2/5,0]
xrange = np.arange(-5,10)
ax[0,2].plot(xrange,np.poly1d(mm)(xrange),c='y')
Out[106]:
In [107]:
df1,Ldf1,ax,p = ut.check_yz(df,Ldf,mm=mm)
In [108]:
df2,Ldf2,mm,ax = ut.ch_vertex(df1,Ldf1)
In [109]:
save_both(k,df2,Ldf2[0])
In [110]:
model = save_model(k,mm,model)
2¶
In [111]:
k,df,Ldf,ax = start('2')
In [112]:
mm = fit_model(ax[0,1],df)
In [113]:
save_both(k,df,Ldf[0])
In [114]:
model = save_model(k,mm,model)
Model¶
In [115]:
model
Out[115]:
In [116]:
model.to_csv(os.path.join(outdir,'model.csv'))
In [117]:
outdir
Out[117]: